Seriously, it's not me.
I taught him how to "delete hole" and he was psyched because it saved him time.  But he gave up on it since because it doesn't always slide over ALL the midi data for some reason EVEN THO he selected all tracks.   
For example, in his orchestration, it might delete two measure successsfully and slide over all the notes, automation, meter changes, etc., EXCEPT for two tracks that WERE selected.   I wouldn't believe it, but he showed me.  Then I tried it on his machine and it happened to me too.
 
I don't think I've had this problem on my machine, but I work with mostly audio, while he works with mostly midi.   He's on X1 and I'm on X3 (but i don't recall the problem when I was on X1).  
 
One thing i was going to suggest to him was bouncing all midi data to clips  before trying to delete a hole.  It seemed to possibly be related to whether or not the offending tracks had midi data in the deleted region........  not sure.....

I have this friend see.......
 
I stopped reading at that point
 
 
 
 
Only joking.
A couple of things spring to mind.
 
Was there a visible "gap" on these 2 tracks midi clips where the hole is?
In other words (this is so much easier to demonstrate than talk about) if the 2 tracks in question were abutted rihht up against 01:01:000 then there's nowhere for them to go.
 
Another thing, were either of these clips locked? Locking I'm  sure would prevent them from sliding across

I'll check.... I MEAN, I'll ask my.. friend.

They have creams that'll clear that right up. ;-)
 
Seriously though I'd say this sounds like the Selection Bug but I don't recall that creeping in until X2. Mind you I did not work with X1 for very long. Perhaps that issue has been there longer than I thought.